text:
How to deal with an advisor who wants a "friendlier" relationship with me than I do?
I work as an assistant at a university in Australia. I joined the team consisting of my current advisor and his two PhD students. The other group members are men and they have a co-worker-like relationship with him. At first it was good, my advisor was very helpful (I have worked there about ten months and I published two papers with him, both in journals with a high impact factor). But when we started to get to know each other better, it unfortunately changed. I am a young woman and am afraid that he wants me to become romantically involved with him.
I try to keep this relationship work-only, as it’s the most healthy way, in my opinion, but sometimes my advisor seems to think differently. Here are some of the things that have made me think my advisor wants a romantic relationship with me:

He comes to my room very often with no research-related reason and wants to talk, talk, talk about everything but work.
Once, when I was busy working, he came to my room and asked if he could take a photo of me. I felt ashamed and did know what to say and then finally, he took the photo.
Sometimes I think he is mad at me that I want to keep this relationship work-only, and then does not answer my emails about our research.
He is very careful with all this, says those things only when we're together. A while ago I heard that his PhD student suggested to him that he spends too much time with me. He laughed and said it's not his business, and that we are working hard on some novel research method.

My advisor has powerful connections here at the university and I'm afraid no one is able to do anything about it. I’m only interested in having a professional relationship with him. However, I’m afraid that if I don’t agree to be his “very close friend,” he will try to kick me out of the university.
I can not move to a different city because of some family issues and can not change my advisor since he is the only person at the university who works on the research I’m interested in. What can I do?

@justme: You might want to add these aspects to the question since they make a huge difference. Also, I am wondering whether you might get better answers to this on the Workplace. (Not that I consider it to be off-topic here, as advisee–advisor relationships are not exactly the same as employee–employer relationships.)

I agree, the sexual/romantic aspects of "close friends", it is best to just say that.

You should know that although women are often the target of this sort of thing, men completely understand this I feel a "tightness in my chest" from reading your account which is why I wouldn't do that (among other reasons). The discomfort of the situation is very obvious. The advisor is lacking in basic empathy, never mind ethics: he is unaware in how his behaviors affect others. That is the source of the difficulty, because it raises the implicit question: can he even be made properly aware.

Maybe your indifference makes him think that you are testing his persistence.

From your title I initially reacted "oh, if only I'd had that problem", but alas, yours is not the good kind of friendliness.  This sounds rather unprofessional.

@venny: ah, the old "no means maybe" routine, or even the "looking really uncomfortable and not responding to my inappropriate advances that I've cleverly made plausibly-deniable so that if you straight say 'no' I can pretend you're imagining the whole thing and if you don't I can proceed as if you're potentially interested, means maybe" routine. I'm not saying people don't think this, but it's still a delusion.

This is a horrible story. His behavior is completely inappropriate, especially knowing the strong hierarchical component to it. I truly hope you will find a way out of this.

I'd love to hear from somebody w/ experience in Australian academics to know if these answers being given are relevant.  To me they seem presumptuous in assuming Australia brings the hammer down on stuff like this like they do in the US...I'm curious if that's truly the case because I'm worried she's going to be ostracized by an influential professor who's already shown to have no problem ignoring research-related communication.

There should be a tag .

related and relevant?: http://science.slashdot.org/story/14/09/19/1548209/science-has-a-sexual-assault-problem - Survey of Academic Field Experiences (SAFE): Trainees Report Harassment and Assault

@justme I've skimmed through most answers and comments and most lack one thing. Informality.
First, before going for very serious and consequential measures like filing a report for Harassment, you should try to solve this informally. Every person deserves a modicum of respect and justice. Your advisor may even not be aware that his interest in you is not being reciprocated. There are people like that.
1st Casually release the info that you already have a boyfriend, or someone you already have a commitment. Most of the times this is enough for the attempts to stop.

(REsuming 1st solution) Or you could just say, as if your disclosing casually in a conversation, that you're at a point in time, when you're not looking for any relationships, and you just want to devote yourself to research or something similar. (this is the tread soft solution)
2nd If still, he continues with the attempts, tell him, straight on, that you're just not into him and that you feel it's not proper to get into a romantic involvement with your advisor.
3rd if nothin of the above works, go for the filing the report/complaint.

@Anoldmaninthesea. The 3 most up-voted answers suggest informal approaches, none of them mention filing a report for harassment as the first step. The 'fake boyfriend' approach is a terrible advice as discussed below.

@Jigg, if by informal you mean 'calling a meeting' wow! And the 2nd most voted seems to be based a bit too much on his/her personal experience. It seems as if the author, had experience only with very ill-intent and relentless people that would go after someone even after knowing they had relationship.

@coburne I agree with you that it would be good to hear from an Australian academic but I disagree with you that women are protected in the US.

@jww I'm not saying that it's risk-free, but the 'fake boyfriend' scheme will fail for the reasons listed below. Not to mention it's highly problematic on the principle. Frankly, it's unlikely that OP will sustain this abusive relationship until she graduates. If making her advisor act like a grown up prevents him from working with her, maybe it's better if he doesn't.

@jww fear of retaliation and deference for advisors is vastly exaggerated among graduate students. This is a western country where women don't get sacked for asking to be treated with respect. In a private company, creepy-advisor here would face serious consequences and it's time academics get treated with the same standards. This is especially true in departments that host virulent gender equality advocates.

The word integrity comes to mind. Which, of course, means not only selecting what you think is the morally correct course of action, but being able to face the aftereffects of your decision. I'm so sorry that you're in this position to begin with. But as long as you pick the choice that you'll be most proud of 10, 20, 30 years down the road, you'll come out okay. Good luck to you.

An advisor like this is a total d-bag.

Just one small thing(not sufficient to be an answer of its own), If you choose to take formal action about this(I don't want to take a stance on whether you should or not, just saying if you do...), I recommend beforehand getting something in writing from him discussing your current performance. That way, after you do whatever you do, if his attitude towards you suddenly changes as a result, you have proof of this attitude change, and it isn't just his word against yours.

Update desperately needed. What happened?

I wish people would come here afterwards and tells us how they proceeded and what were the consequences of the decision. These types of questions always end on a permanent cliffhanger.

Asking for "something in writing from him discussing your current performance" has the risk of him wondering why you are requesting it.  But perhaps you could get another professor to think up a plausible reason for asking without revealing that you were the one wanting it.

I don't know if a meeting at which you "set the agenda" would be particularly helpful at this stage. It might make him feel "attacked", put him on the defensive, and he may retaliate against you in response. (I'm not suggesting that he would try to get you kicked out of the university or the department; there are many, many other small and large ways an advisor can make things difficult for a student. You already suggested that when he's mad at you, he deliberately ignores you emails, for example.)
I strongly disagree with the advice to flaunt a (real or fake) relationship, to let your advisor know you're unavailable. I've seen people try this, and in my experience, when applied to someone who does not respect boundaries, the outcome is often that then he starts asking you a whole lot of very uncomfortable questions about your boyfriend and the relationship.
Also, he's probably doing this because he enjoys it (flirting, the chase, whatever), not because he wants an actual committed relationship. So I'm not convinced that he would be dissuaded by your unavailability.
Instead, I suggest you start using a variation on the following phrase to respond when he does something that makes you uncomfortable:

I don't want this. This makes me really uncomfortable.

As in,

I don't want you to take my photo. Please don't ask again, it makes me really uncomfortable.

or

I don't want to talk about my personal life with you. It makes me really uncomfortable.

etc.
And, if he persists in whatever is making you uncomfortable,

I need to go (get a cup of coffee/make a phone call/talk to another student before he leaves for the day/make some photocopies/etc.)

then remove yourself from the situation.
I recommend practicing saying these words on your own, until they feel natural. This will help you feel less flustered when a situation comes up.
I also concur with StrongBad's suggestion:

I would suggest the OP writes down every time she tells the advisor he made her feel uncomfortable. She should also keep track of times he makes her feel uncomfortable in which she was uncomfortable telling him he made her feel uncomfortable.

and I would add, also make a note of who else (if anyone) was there at the time.
This will help in two ways:

You'll be able to tell if the situation is getting better or worse with time.
If you do need to escalate at some point, you'll have some documentation.

I think this is the best approach, but I also think at some point the OP needs to stop telling the advisor that he makes her feel uncomfortable and escalate things. At this point documentation would be really helpful. So to add to your answer, I would suggest the OP writes down every time she tells the advisor he made her feel uncomfortable. She should also keep track of times he makes her feel uncomfortable in which she was uncomfortable telling him he made her feel uncomfortable.

@StrongBad good suggestion! And I added, also note who else was there (i.e. potential witness)

If pushed further to explain why you are uncomfortable, you can say that it is for personal reasons that you do not wish to discuss. And recenter to what it matters research. "Let's keep our discussions to the research. Talking about personal issue makes me uncomfortable (for personal reasons I do not wish /cannot discuss. We are excellent collaborators and produce wonderful research. Speaking of wish, what do you think about the last experiments?" "Please do not take picture of me. It makes me uncomfortable for the reasons I cannot discuss...." Hopefully only the the first sentence is enough.

@StrongBad - Just out of curiosity, what are you advising the OP, to be planning to do with that documentation?

@New_new_newbie I added an answer. If the harassment continues I would report it to the department chair, HR, or the ombudsman. Being able to say these are when and how I was harassed will go a long way towards resolving he-said/she-said conflicts.

I agree with being direct. But if the issue is to be not taken as "attacking" or singling out the advisor, it may be better to stick to "general" statements: "I prefer not to talk about my personal life in the workplace." or "Unless it is for an official website, I prefer not having photos taken in the office." and if there is question "Why?" then "Splitting work and personal life makes me happy and productive.".

I guess this is really the best solution. The first solution is "too" German! 1 hour direct meeting!!! hahaha I couldn't stop laughing when I read the meeting thing!!!

A "mixed" review. -1 f"or he's probably doing this because he enjoys it (flirting, the chase, whatever), not because he wants an actual committed relationship." that I feel is too light. +1 for some good practical advice. On balance, a "0" from me, but with maximum "variance."

Preliminaries:
You are in a tough spot and I don't think that any course of action is ideal or without risk.  If you can accept this "messiness" and commit to a reasonable course of action, you'll probably come out OK. It's also important to understand that you can't control or determine his reactions, and you can't be responsible for his feelings, as long as you act responsibly and ethically.
Call a meeting, set the agenda
First, I suggest that you schedule a meeting with him to discuss your working relationship.  If it were me, I'd speak plainly and directly, without any tone or implication of blame or distress. I suggest that you make these two points:

"I just want to confirm that our relationship is about work only. I am completely focused on my research career, and that is the basis for our relationship.  I'm not here for friendship or anything else."
"I'd like to make changes in specific behavior patterns.  In these requests, I may be different than other PhD students, but I'm clear about what I need and what I'm comfortable with."  Then list the behaviors you'd like to see changed (e.g. no "pop-in" meetings with non-work discussions).

Having a successful meeting
Schedule this meeting.  Don't improvise.  Don't combine it with any other meeting or topic.  Allow for enough time (an hour is sufficient, though you may only need 5 minutes. By scheduling an hour, you are avoiding time pressure for everyone involved) without pressure to complete sooner or worries about starting on time. Plan what you are going to say ahead of time, and even rehearse it, by yourself or with a friend.  If you think it's necessary, have an ally with you at the meeting -- a woman friend, anyone you respect in any role in the University, or even someone from the outside.  Just say, "This may be a difficult conversation, and having X here to support us gives me more confidence."
Also, if you can imagine that you are asking for something innocuous -- e.g. changing the seating arrangement at a seminar, adding vegetarian options at a department meeting, etc. -- it will help you and it will help him immensely.
You don't need to ask him how he feels about you, to discuss the past or what he was or was not thinking or intending at the past, or any of that.  You also don't need to explain how you feel (even though it would be justified).  Talking about your feelings in this setting is almost never effective to change behavior.
You don't need to ask him if he's "OK" with your requests, or what he might want as an alternative. There are no alternatives. What he wants beyond your requests is irrelevant.
Also, if he brings up any other subject, no matter how related or how reasonable, you say: "I'm not here to discuss that."
If you haven't picked up on this already: you need to be the dominant person in this interaction. Not flamboyantly or even demonstrably.  Just set the agenda, run the conversation, and lead to the conclusion.
Yes, you will be nervous.  Yes, you might feel uncomfortable.  Yes, you might be seeking his approval and affirmation during this meeting. Let go of all of that. All that matters is that you have this conversation -- short, to-the-point, and direct -- and get to the conclusion you are aiming for.
Finally, if he wants to talk about his needs or experience in the relationship, do that in a separate meeting. Be firm.
Be prepared to set boundaries
Regardless how the meeting goes, it's likely that he'll continue some or all of the behaviors, if only out of habit or faint hope. For each setting and behavior, be prepared to set a boundary -- saying 'no', disengaging, leaving the room, reminding him that you are not 'OK' with this, or what ever you believe will be effective.  Not to put him down, but imagine that you are training a dog to not bark or to not jump on visitors.  It's just behavioral conditioning.

If you do all this in a way that doesn't publicly embarrass him or privately make him "the Bad Guy", it's unlikely that he will kick you out of the department or university.  There's a chance that he might do something bad toward you (many women have experienced negative consequences in similar circumstances), but the odds are lower by taking this path.

Many of the other answers and comments have expressed the view that this direct approach is "incredibly risky" or "likely to backfire" and have suggested more subtle or indirect approaches, including being as "nice" as possible during the process to avoid negative reactions.
My answer reflects my personal and professional values and also my work history (many decades in high tech industry). I'm not naive about power or politics in university departments or research labs.
I believe that it's very valuable and proper for less powerful people to stand up to people in power on issues such as morality, ethics, and even suggestions on fixing problems in the organization (e.g. workload imbalance).  'Standing up" helps the organization as a whole and can be part of a culture change in the organization.
Any professional relationship like this merits a one hour face-to-face meeting if the meeting is about improving the working relationship. Just because the topic might be uncomfortable to one or both doesn't change that. (Such a meeting need not be a "trial" or "attack" as some people have described it.)
One problem I have with indirect/subtle approaches in this setting is that they do not adequately empower OP, implying that she needs to be deferential to her adviser in this matter. I believe that, in the matter of relationship integrity, no one has to be deferential to anyone else.  We all have the right (and duty) to stand up for ourselves.
Last, I don't assume that the adviser is a harasser or that he is doing anything that he considers inappropriate.  It all may be very innocent and even well-intentioned on his part. If he is well-intentioned, then he'll probably receive these direct communications positively, shift his behavior, and all will be well.

This seems like excellent advice to me. Also, see if you have a women's centre on campus. If so, they may have additional advice about the process to follow in case you need to make a formal complaint later.

@Kai the OP said in the question, "I can not change my advisor" - presumably she has considered it and determined that she can't

+1 Also inform other people (e.g. your family) about what you are facing. If you already have a boyfriend, arrange for him to pick you up (as often as possible) from the lab, to emphasize your "unavailability". That might also work with any male friend (the supervisor does not need to know he is not really your boyfriend). You can also arrange for your family (mother, father, brother) sometimes to pick you up. Having a strong support system (family, friends) discourages this type of behavior.

After the conversion, send him an email outlining the agreement: "Thank for you meeting with me today and agreeing to keep discussions limited to research topics only.". If it comes that you need to deal with HR later on, the paper trail is the key. Your discussion should also discuss friendly way to reminding him to stick to the rules. So, next time he wanders off to your office, you can refer in a friendly way to the agreement. Stay calm, strong, and smile.

If you do this it will surely cause you difficulty: please be more nuanced. Unfortunate as this is, unless he does something overtly inappropriate, you need to stay strong. if he comes and talks to you while you are busy working, just say "Hey I really need to get this done now, perhaps I we can talk about work some some other time". Do thing things you would do if you felt like another coworker(equal) were hitting on you, but cared about their feelings. Try and give him a hint.

@Neo -- I don't believe your suggestion -- "...give him a hint" -- will work. He hasn't picked up on her hints so far. I'd bet he won't pick up on any further hints. Besides, the direct approach I'm suggesting is very compatible with "caring about his feelings". Regardless of his yearnings, it's in his best interest to not violate her boundaries and to have a mutually successful work relationship.

@Alexandros:  I don't like your suggestion that the OP have her boyfriend (if she has one) pick her up to demonstrate her 'unavailability'.  The fact that she is not interested in anything more than a professional relationship with her supervisor should be sufficient.  Demonstrating 'unavailability' in this way reinforces the culture of a woman only being off-limits if she is already 'taken' by another man.  There's a nice webcomic about this, but I can't find it right now, so this article will have to do.

@TaraB The boyfriend or a family member picking the OP from the lab, signifies two major things, besides unavailability: a) That the problem is known to more people outside the OP and her supervisor b) That if things get ugly, the supervisor has to worry not only for the OP's reaction but her support system's (family, boyfriends) reaction, as well. Both of those reasons are strong enough for both "love-sick" supervisors to full-fledged sexual harassers to reconsider in fear of retaliation, either in form of legal action or getting their ass kicked in a back alley (which I don't suggest)

@TaraB Also remember that typical sexual harassers want to keep the whole situation secret. The OP should not deal with this alone. That is what her supervisor wants her to do. She has done nothing wrong, so she should not keep it a secret. The more people they know and can help (even by showing up to pick her up) the better.

@Alexandros:  Did you have a look at the article I linked to?

@TaraB Yes, but I disagree. As a man, I admit that there are some problems I cannot handle myself. In those cases I seek help from those I love: My family. Why is this different for a woman? Some problems are more easy to handle as a team (with your boyfriend, husband or family) instead of trying to handle it alone. And do not forget that sexual harassers sometimes get aroused from women turning them down and further escalate their approaches. But the fear of getting their asses kicked might be a stronger "incentive" to stop their predatory behaviour.

Just to clarify: I didn't mean that the meeting you propose is an attack, just that the advisor might perceive it as such. My experience as a mod here has taught me that people can feel attacked very easily :(

@ff524 - Yes, I understand the distinction. In my opinion, OP shouldn't make her choices based on whether some act will or will not be perceived negatively. That sort of second-guessing can lead to actions that are less than effective. If she acts with integrity and keeps the conversation emotionally neutral, then any perceptions of attack can be dissipated.

If it's important to the OP to avoid negative repercussions, then I definitely think she should weigh how others are likely to react! I don't mean to say that your approach is necessarily unwarranted, but it is very clearly more likely to prompt a negative reaction, if the professor is as unprofessional as the OP perceives him to be

@ff524 -- I'm not saying that she should not be aware of possible reactions. I believe that there are potential negative consequences and reactions to all possible courses of actions. For example, it's very common for people to get offended or angry from subtle rebuffs or "fibbing" ("I have a boyfriend"). Subtle approaches risk misunderstanding and misinterpretation.

@Alexandros: You write: "As a man, I admit that there are some problems I cannot handle myself. In those cases I seek help from those I love: My family." I cannot think of a single professional problem in which I would want or need to involve my family because I can't handle it myself.  What would be such a situation for you?

I also find the "asses kicked" part of your answer troubling.  For all we know, the OP is a proficient martial artist and entirely capable of kicking her advisor's ass.  Is that in any way a reasonable or helpful option?  If not, why is it better to hint at this threat on the part of some auxiliary male figure?  (In't it worse?) On a personal note, not once in my life have I thought "Boy, I would really like to date this woman.  Too bad I can't act on it because I think Mr. X might kick my ass."

@Alexandros:  What Pete said. =]  (I was too busy working to respond to your comments earlier.)

Interesting answer. I find your suggestion of an hour-long meeting to be quite bizarre, though, and at odds with your later suggestion to keep the meeting "short and to-the-point". This matter can be resolved in five or ten minutes.

@LightnessRacesinOrbit - I edited my answer to clarify. The reason for scheduling an hour is to avoid time pressure. Though it could be over in 5 minutes, it's not a good idea to ask for 5 or 10 minutes, because then it will be shoe-horned in between other activities and you won't get quality of attention or conversation that this topic needs. Besides, giving the adviser back 55 minutes of unused meeting time is usually seen as a "gift".

@MrMeritology: "Scheduling" this and indicating that you think it might take an hour to ask someone to stop going out of their way to spend time with you is .... kinda weird behaviour.

@LightnessRacesinOrbit - It's not weird in the slightest.  It's professional behavior, suitable for a serious conversation. Allowing extra time is very prudent, since there's no predicting just how the conversation might unfold.  Rushing or feeling time pressure is very bad under such circumstances.

@MrMeritology: Jumping to a "serious" conversation having never mentioned it before nor made any basic social attempts at evasion is weird. The majority of problems can and should be resolved long before you reach "official sit-down meeting" stage, a point which can irreparably harm your job/study if you are not very, very careful.

@LightnessRacesinOrbit While that's probably true for most problems, this clearly has surpassed that level.  The point of making it an official meeting and scheduling plenty of time for it is to underline how significant it is.  She clearly has made some basic social attempts at evasion.  Further, it's very common for it to be nearly impossible for people in this kind of situation to be unable to do as you say: harassers can easily make the harassee uncomfortable about rejecting the advances.  Sit down meeting is exactly what this problem needs.

"She clearly has made some basic social attempts at evasion." Can you provide some examples of this from the question? As for "harassers", this is kinda my point: most people here are jumping the gun by accusing this guy of "harassment", but I feel that this is a growing problem: I see no categorical evidence of "harassment" here, only unrequited friendliness that has yet to be appropriately deflected, and suddenly the guy is a sexual creep? That hardly seems fair at all. In fact, this sort of attitude causes a lot of problems for guys in work nowadays. Let's not get cavalier, is all.

@LightnessRacesinOrbit - It just sounds to me like he's recommending she approach the issue with care and respect. Chances are, the advisor has good intentions, like others have said. Scheduling the extra time gives the advisor some cool-down time. He might use that time to go be alone and process his feelings before he has to go teach a class, meet with his boss, or whatever it is he might have to do 55 minutes later. In short, this allows the op to be assertive, still be respectful, and also decrease the likelihood of the work part of the relationship being damaged.

Or you could just use normal, basic social engineering first, like humans have for thousands of years!

@LightnessRacesinOrbit: Why should OP have to do something in a backwards and disempowering way just because humans have done it that way for thousands of years? Progress is about understanding that the ways we've done things for thousands of years are not inherently right and should be evaluated under a lens of social justice, and abolished if that lens reveals they're rotten.

@R.. It is not "backwards" and it is not "disempowering". Stop trying to look for and/or create problems. This isn't the right way to go about it just because it's been done for thousands of years: quite the opposite. It's been done for thousands of years because it's the right way to go about it. Stropping around making meetings and ordering people not to behave in a certain way, before you've even attempted simple social mechanics, is neither the best approach to getting what you want, nor is it "progress". It makes you look ridiculous and melodramatic.

@LightnessRacesinOrbit: Being treated with fairness and decency should not be a privilege reserved to those who are skilled in social engineering. If the advisor is behaving in a way that even some students would not be able to defend themselves from, then he is a problem, and he needs to be made aware of this and told to stop.

@R.. I never disputed that. I'm simply saying that there are more effective and appropriate ways to achieve that goal and to resolve the problem, than immediately kicking up a massive, loud and obvious fuss about it. Of course if that approach doesn't work (or if the OP, for whatever reason, feels unable to do it) then take it to the next level, but don't jump to such substantial measures from the off. There's simply no need.

I think you need a bit of both: somehow make it absolutely clear that to you, this relationship is work-only, and that the advisor's behavior is making you uncomfortable for that reason - but without making a fuss about it or being confrontational about it. So you need to be resolved in your mind how to go about it, and the message must be clear, but that doesn't mean it has to be heavy-handed.

Generally, I think this advice doesn't leave room for the possibility that this advisor simply doesn't realize what he's doing - this seems quite likely to me, and in that case, some gentle nudging may be all it takes, so I'd try that first.

@LightnessRacesinOrbit, did you miss the point where he came to her room and asked to take a photograph of her? Which she then said she was uncomfortable with? Yea that sounds pretty creepy to me.

@ryan: I never said it was not creepy.

Whatever you do, please ignore the advice given by some people here to demonstrate your 'unavailability' to your advisor by talking about having a boyfriend, or having your boyfriend or some male friend come and pick you up from work.
You don't need any 'excuse' to be uninterested in having anything more than a professional relationship with your advisor, and to imply that the main reason you are uninterested is because you have a boyfriend might suggest that you would be open to the idea of a romantic relationship with him if you were 'available'.
On the whole, I agree with most of ff524's answer, although I personally would be very uncomfortable with telling someone that they were making me feel uncomfortable, so I would be unlikely to use the suggested phrase.  What I would do is simply say 'No' to requests such as taking a photo of you.  You don't need to give any justification for denying an odd request.
You may need to address the issue directly with your advisor, just because it's going to keep making you feel uncomfortable, and most likely have a negative effect on your working relationship.  I don't know the best way to go about this, but your university probably has some kind of counselling service that could help.

While it is important to minimize the discomfort in the the already uncomfortable situation, I think it is best to say something beyond just "no" to make it clear that the behaviour is both unwanted and unacceptable.

From the fact that the OP's advisor did in fact end up taking a photo of her due to her not knowing what to say, I think that a simple 'No' would be a big step in the right direction.

I think if it happened to me, my response to the photo request would actually be 'What for?'.

I agree that a plain "No" is infinitely better than not raising any objection, but for people you'll have years of interactions with (not just some random guy hitting on you) I find it more productive to express "this behavior is harmful to me" to differentiate from "I'm not in the mood right now/I'm photophobic/I'm too tired to talk to you now" etc

I strongly agree with your first paragraph.  Signalling unavailability by calling attention to your partner is a good strategy in many social contexts: most (not all) people would stop romantic pursuit for this reason without feeling personally rejected.  However, in a professional situation, "I'm here to work" is by far the better response: not only for the OP but for other professional women.  Whether the OP has another romantic relationship is information best left out of a workplace situation that has gotten too familiar.  Pretending that she does is alarmingly unfeminist behavior.

@PeteL.Clark:  I overall agree very much with your comment, except that I'm not sure that I agree that calling attention to one's partner is ever a good strategy to avoid romantic pursuit.  Since most of the time the person being 'pursued' probably wouldn't be interested anyway, the existence of a partner is kind of a red herring.  I don't actually see the problem with feeling personally rejected (for a romantic relationship).  Not all pairs of people are suited to becoming couples, and that's just the way it is.

Yes, but those are not by any means the only options!  This is becoming like my refrain or something, but a simple 'No' is quite sufficient.

@Tara B: In a professional context, a simple "No" is quite sufficient.  In...well, we've already agreed on the only relevant case, so let's leave it at that.

Given the scope, I guess I'll leave it at that if you want to.  Although since you strike me as someone who cares about feminism, you may like to read this article if you haven't already seen something similar.

Let us continue this discussion in chat.

"to imply that the main reason you are uninterested is because you have a boyfriend might suggest that you would be open to the idea of a romantic relationship with him if you were 'available'." No, I don't think so. Most men recognise this line as a polite "I'm not interested" and recognise that the OP may or may not actually be taken. And let's drop the sexism accusations around this topic (as seen in other answers): it works both ways.

@LightnessRacesinOrbit - I had the same opinion. But my advice, which was in essence ''suggest unavailability and leave it there, you don't have to confront'' received 7 down-votes and confrontational advice is getting rampantly up-voted! I always thought confrontation can be a plan B -- if all else fails. But maybe these down-votes, and this post which starts-by-bemoaning-that-thought-process sitting at +20, means people like us are a minority over here and maybe we should chicken out of here to avoid inviting some fancy name calling. Thanks for sharing your opinion anyways :)

Secondly, as in the comments below inkka's answer, 'suggest unavailability' is being painted as saying ''women are available unless already taken'', which we never intended to say. Thus, out of nowhere, a gender debate enters the picture. Absolutely hopeless :(

"I'm sorry Dave, I'm afraid I can't do that"

I think a lot of advice that people are giving is unwise.  While I am sure they wish to be helpful, I am not sure they are qualified.  I have been active in the women in technology community for 25 years, which does not give me all of the answers but does make me more aware of what can go wrong than some of the other respondents may be.

You need a support group of women in your field.  In computer
science, there is a great email list, Systers, whose members
frequently solicit and give advice based on experience, not just
theories.  Find something like this in your field.  Ask someone to
post anonymously for you, since it would be unwise to let your
identity be known.
Second, as others have said, document everything.
Find out if your school has an ombudsperson, graduate women advisor, equal opportunity officer, or the Australian equivalent. (I'm American.)  Such people can often give useful advice.
Try to build ties with other graduate students and faculty in your department.  You may need allies.  The other faculty will know your advisor's history and how best to deal with him.  Tenured faculty will be more able to help than untenured or adjunct faculty.  While female faculty are your natural allies, don't overlook male faculty, especially ones with large numbers of female students who have not had problems with him.
I do not recommend confrontation.  Backing someone into a corner is dangerous; allowing someone to save face is safer.  I think it's fine to ask why if he asks to take your photograph, but I wouldn't sit him down and demand that he stop treating you inappropriately.  Prepare remarks that you can say if needed, such as:

"I'd prefer that the office door be open."  (If asked why, say because you'd feel more comfortable.)
"The women's center advises female students not to socialize with their advisor without other students present, since someone might get the wrong idea."

So many +1s.  Alas, I can only give one.

I do not recommend confrontation. Backing someone into a corner is dangerous; allowing someone to save face is safer exactly

I am not convinced that he wants a romantic relationship with you. Rather he is boosting his ego by flirting with you and actually enjoys flirting with you.
Your response need to be adequate to the situation. You should respond to amateurism by professionalism
I think calling a general meeting of an hour to set things straight can backfire, because it will sound like a trial to almost anybody. And in a trial, the defendant defends itself.
Rather, you need to cool him down over an extended period of time. Try not to over-think.

He comes to my room very often with no research-related reason and
  wants to talk, talk, talk about everything but work.

Delay. You are in the middle of something important, and he needs to know that. Just tell him that you need to round up with what you are currently doing and that you are willing to go full gossip at the coffee break.
Set boundaries. You haven't said what he is talking about. It is mostly about you? Then when it cross boundary you just say it is personal. Don't break under any "Oh come on" pressure tactic.
Be a good listener. It may surprise you, but you also have the power to direct the conversation to a subject of your liking. By listening well to what he said you can go deeper in a harmless topic, one which doesn't make you feel uncomfortable.
Stop the break when your mug is empty, excuse yourself and go back to work. It is important that all this chitchat happens far from your desk. Desk = work, coffee machine = small talk of at most x minutes.
Invite other staff to the break talk. Don't do it systematically, but sometimes drop by someone's else desk and invite him\her too. It will obviously annoy the shit out of your advisor. Note: At least this works for me. That's where he will show his true color. Either he will invite you offsite, an invite that you can decline, or tell you not to invite other people. That's all you need to hit the ethic institution at your university.

Once, when I was busy working, he came to my room and asked if he
  could take a photo of me. I felt ashamed and did know that to say and
  finally, he took the photo.

I am sure the first thing which came to your mind was "Why?". You should probably tell what's in your mind.
Why do you need a photo? It is for the lab website, or a publication? Can we do that at the break or later? Thanks

Sometimes I think he is mad at me that I want to keep this
  relationship work-only, and then does not answer my emails about our
  research.

Again we don't have much information about the context. But I will advise you to read How To Win Friends And Influence People. Don't get turned off by the title. It is not a guide to become a manipulative asshole.
Remember that there is politics at the lab and the office. The other lab members are gradually building resentment towards you for your "preferential treatment". You need to take this in account as well.

This is spot on. You just gradually reduce his interest by making your own lack of interest clear, subtly and gently over a period of a few weeks: he'll quite soon get the message. It's not a workplace-specific thing, it's just basic social behaviour. I'm not sure why some other answerers are recommending some pretty draconian measures as if this were some form of sexual assault. It's not. It's a person being friendly to another person. If the other person doesn't want that then they should steer the relationship in another direction.

+1 because some of these unavailability suggesting tactics are very good.

@LightnessRacesinOrbit it is a workplace thing because he is her advisor. He's not a fellow student, but holds real power over her. As such, he should err on the side of caution. Taking a photo crosses the line imo.

@TemplateRex: Many people hold real power over many other people, in and out of the workplace. None of that changes the best way to deal with the situation, at least not in the first instance.

+1 for turning every interaction into a professional one - though it sounds like this advisor doesn't respond well to subtlety... When he comes for a chat, something less ambiguous might work like "Sorry, I can't talk right now, but if you tell me what the agenda is for this meeting, I can put something in the diary?".

As an added suggestion, keep a list of questions and discussion points on your desk, all directly related to your research. Any time he enters your office and talks about anything other than your research, you are glad he has some free time because you have these things you need to discuss with him.

-1: I feel this answer is far more focused on the questioning the victim than on understanding or responding to the problem as outlined in the post. Nor have I ever in my professional career or personal life seen these kinds of 'delaying tactics' work to rebuff the inappropriate attentions of men acting like this. What I see all too often is women using these tactics without success followed eventually by a direct confrontation in which the perpetrator complains that the victim should have used these tactics instead of resorted something so direct.

First, if this advisor has any stalker-like tendencies (insufficient information here to determine that conclusively, but my hackles have been raised by several things in the original question), bringing up another romantic relationship, real or ruse, will NOT make this person leave you alone and resume a more professional relationship. I know this goes against all the tropes of feminist empowerment, but you need to be prepared to lose this job and your "career" in order to protect your personal safety. No career is worth sacrificing that. Only the young and foolish live with such absolutes in their mind that their career will be permanently destroyed by one individual within an academic ivory tower or cloistered business community. Those who are hardworking and talented can generally find a new path to success. I know this from personal experience.
With that said, I agree that you need to clear the air in a manner like MrMeritology and Tara B have suggested: openly discuss the matter in a non-threatening but direct manner, and meet any further incursions beyond the boundaries of your comfort zone with firm, unambiguous answers of "No". I also believe ANY discussion of this matter with the advisor needs to be documented, and not just via written memos. If this person is merely socially inept or a garden-variety amateur stalker, a paper trail may be enough to damn him if he should mount a personal attack, as such people aren't often very good liars. If he is vindictive/manipulative in his daily dealings with people, you may be dealing with a person with sociopathic tendencies, and they are usually VERY convincing liars. I recommend the use of recording media, audio and/or video. People can play off the written word as being exaggerated, misinterpreted, or lacking context, but recordings which include inflection and tone (audio) and/or body language (video) are much harder to shrug off. I know that some may raise concerns about privacy and wiretapping laws, but unless you need to escalate and share such recordings with the appropriate authority, such concerns are trivial, in my opinion.
As I have gathered from the question, the advisor only engages in this behavior when he is alone with you, so no witnesses and we are left with a he said/she said situation. In such situations, a recording device becomes as close to an objective witness as you can get. If you take the route of recording the uncomfortable encounters or meetings to discuss this issue, make sure to get as clean a recording as possible, never share with this person that you have made or are making such recordings (though please keep a close friend or family member in the loop about this situation), and ONLY use such recordings with the AUTHORITIES (Academic, Civil, Criminal) as a last resort, to ensure your personal safety and to protect yourself from liability should he try to retaliate.
Finally, I cannot overemphasize enough: if any tactic you take does not work after a few weeks/months, you need to reexamine the importance of this particular career path versus your personal emotional well-being and safety and determine which is more important. That may not be what you want to hear, and I hope I am over-reacting to the situation, but what you are describing has a fifty-fifty chance of being more than a harmless flirtation by a socially-inept academic. The only way to figure that one out is to take the bull by the horns and politely confront the advisor and his behavior, as has been suggested by others.

+1 for this sentence: Only the young and foolish live with such absolutes in their mind that their career will be permanently destroyed by one individual within an academic ivory tower or cloistered business community. I have been through this situation when my career was ruined and I have re-established it.

I feel that you should add some phrasing about finding out if it's legal to make a recording without the other person's knowledge.  In the US, the legality of doing this varies from state to state.  According to this link it sounds like it's ok in Australia as long as you are one of the participants in the conversation (this is the law in Texas as well, for example) http://www.austlii.edu.au/au/legis/qld/consol_act/iopa1971222/s43.html but I still think it might be best for her--or anyone else in this situation, wherever they happen to live--to find out from someone familiar with local law.

I'd like to add a few varied points, and I assume that although not explicitly stated in the answer, the OP gave the usual more-and-less subtle hints but they did not work.
The basic idea is to first arrive at a point that allows a calm decision how to go on, and that also allows you to get in the emotional/mental state of freedom that allows you to tackle the problem e.g. by the meeting @MrMeritology suggests.

One very practical step that may help to avoid/reduce the stressful situations: Can you move into another office where more people work (or have some fellow student move into your office) and thus basically limit the possibilities for him to catch you alone?
On the one hand, others already suggested that this would mean witnesses. On the other hand, it may make him behave.
I fully agree with the say lots of plain "no"s advise by @ff24. I'd go for the shortest and plainest "No" And guess follow up questions ("Why?") would best be answered by "That's none of your business." - possibly re-enforcing "The answer is no, and that has to be enough".
I think super-clear boundaries are required here.
Maybe you can excercise/train these situations with some friends?
Somehow I think it likely that the problem cannot be solved with less drastic measures than the meeting (+ paper/electronic trail) MrMeritology suggests. I guess it would be good to prepare yourseld emotionally for that.
You state that for personal reasons you cannot move away. However, there may be other points where you can gain independence in the sense that you are less vulnerable to the attacks you fear, and more on equal terms for the totally sensible demand you have.

E.g., if you are financially dependent on a work contract in his lab, it may be good to put together some savings that will make you independent (in that they'd allow you to bridge the time till you find something else to earn your living) either have a second job, or speak with your family about support in case of need, or do some superhard saving, or have someone trustworthy who'd give you a job immediately in case of need.
Get yourself connected with colleagues (from your as well as from other groups).

Is the PhD student who spoke about him spending too much time with you trustworthy so you can talk to him about the problems? - this may be a valuable ally.
Colleagues who know you (e.g. know that you are not starting rumours to discredit the supervisor without any base for that but that instead you are harrassed) are most valuable: in the example, they are your best insurance against him starting rumours about you.
Also they can help you with the emotional stress you're subject to.
Knowing the local conditions, they may come up with solutions/help we cannot think of.
And last but not least, being connected with other groups may also open other plan Bs, i.e. changing your research area in case you arrive at the conclusion that the situation is emotionally/personally unbearable and changing to another topic is the lesser evil (I'd actually suggest that there may be other interesting research topics).

Get emotionally as independent as possible. Maybe family/friends can help you to get there. If you are religiously affiliated, such help may also be available as pastoral/spiritual care (obviously depending on denomination and personal relationship), or you can look for a professional coach.
This is not a nice-to-have, but a basic requirement for the actions suggested: you'll need it to say NO, for the meeting, it is what allows your self-esteem to survive in the future if you decide to leave the lab, but also if you decide to stay.

+1 for suggesting moving to a more public or shared office--not a solution, but may make things easier.

Asking to take your photo is truly creepy. I would consider talking to the person or office at your university responsible for sexual harassment charges. Typically universities have a very clear process for dealing with such situations, and it may be that he has done this before. You can discuss with their office how to proceed. They might have some good ideas, and they typically won't act in a way that you are uncomfortable with, if you are worried about repercussions.
Also, I wanted to echo other people's discomfort with the "call a meeting" proposal. This strikes me as incredibly risky. I think it's better to get the appropriate office on your side.
Edit: A couple more ideas:
1) invite someone from HR to give a presentation on workplace ethics (including sexual harassment) to the lab. [Somewhat risky as it might embarrass him in front of the rest of the lab. Perhaps it can be arranged for it to seem like coincidence, not having been arranged by you.]
2) if there a campus pamphlet about this issue, you could leave it in his mailbox, perhaps with appropriate passages highlighted.

I highly doubt that attempting to make something like this seem like coincidence is going to work out in this situation. Especially if he only has the one female advisee--I think he's going to figure out who was responsible.

I deleted the "sneaky" comment and rephrased--I wasn't meaning to imply it was dishonest, just lazy shorthand for the concept of hiding responsibility for the presentation/highlighted document.  My only concern is for the OP's safety, I didn't mean to imply you were suggesting something nefarious, just that it involved hiding information and I didn't think that the information in question would stay hidden in this situation.  Hopefully no hard feelings!

@msouth: Okay, well I withdraw my objection. I definitely agree with your comment that this is risky. There is no easy solution.

I think there are five possible ways of dealing with this situation. I think each has been addressed in separate answers, but no answer contrasts between the different approaches. It seems you could (1) contact the person or department responsible for dealing with claims of sexual harassment, (2) have a conversation with the supervisor about his past behaviour, (3) mention to the supervisor whenever he makes you feel uncomfortable in the future, (4) change your behaviour in a way that makes him harass you less, (5) ignore it.
1. Contact the person or department responsible for dealing with claims of sexual harassment
While I think this is the best way to deal with sexual harassment, it puts considerable burden on the victim and puts the victim at further risk of harassment and retribution. The reason I think this is the best way to deal with harassment, is that if the university does not know about the harassment, they cannot change anything. The more harassment cases the university has to deal with, the more likely they will require supervisors to behave properly and provide support mechanisms to victims. The problem with this approach is universities tend to try and protect themselves and not their employees and students. If you do not have any documentation or evidence of the harassment it becomes a case of he-said/she-said and the university may initially ignore your claims and force you to sue the university.
2. Have a conversation with the supervisor about his past behaviour
I see no advantage of this course of action, despite the answer being highly voted. It is in essence alerting the supervisor to his behaviour and drawing a "line in the sand". If he doesn't change his behaviour, then you have to escalate to reporting him to his superiors. If he cross the line and you do not report him, and as I mentioned reporting him puts you at risk, he will have effectively called your bluff and may feel even more empowered to harass you. The best case scenario for this approach is that he didn't realize you felt harassed and the conversation makes him change his behaviour. I think this, however, can be achieved with approach 3.
3. Mention to the supervisor whenever he makes you feel uncomfortable in the future
By telling the supervisor whenever he makes you feel harassed/uncomfortable that his behaviour is inappropriate, this alerts him to change his behaviour. I would suggest to also email him afterwards to make it clear that you are documenting his behaviour. If he is unaware that his behaviour is unacceptable, then you will have accomplished the same thing as approach 2. If he continues to misbehave, you will be collecting evidence for if/when you decide to take approach 1. Most importantly, by not drawing the line in the sand, it will never appear that you are backing down.
4. Change your behaviour in a way that makes him harass you less
I don't particularly like this approach as it puts all the burden on the victim. If he is harassing you because of the clothes you wear, the company you keep, or your beliefs, changing them may make him stop harassing you. While this is the most non-confrontational approach, and puts you at the least risk of retaliation, it requires the an unreasonable sacrifice by the victim. If you are willing to make that sacrifice, the approach can work.
5. Ignore it
This again is a solution, but requires the victim to make an unreasonable sacrifice.

Firstly, I want to say how sorry I am that you're dealing with this. This behavior is absolutely inappropriate, and it's hard for me to believe that your adviser doesn't already know that he's crossing the lines.
There's plenty of advice here about whether you should take a formal or informal approach, and I'm not really going to weigh in on that. Instead, before you do anything, what I would do is check to see whether your university has an official Ombudsman's Office. This should be an office whose sole purpose is to advocate for the rights of students and workers and to investigate complaints.
I think it's worth discussing, confidentially, with someone in that office before you make any attempts to discuss this with the professor. Tell them your situation, and ask for their advice. That way, you've got a clear record of engagement with the school if things really do hit the fan.
Good luck :)

I really think @espertus 's answer should be the top voted.  In addition to what she says, I would say this:
Consult with a lawyer (at least an initial consultation).  I'm not sure I would trust whatever your institution provides to you as a student (free onsite legal counsel or whatever), because they might be under pressure to encourage people to not make waves (although that question might be worth researching in parallel).
Research law firms in your area.  See if there are any that have particular expertise or experience in academia.  Don't think about the price--you're just going to ask them if they will give you a free consultation to find out whether you need representation and what you should be doing in case you do.
Find out:

What specific behavior crosses a legal line
What kind of
documentation constitutes legal proof of those lines having been
crossed.

Perhaps you could find out similar things about the university's ethics code without making a formal complaint.  Just ask what behavior, exactly, crosses the line, and what documentation is required to prove that this behavior has taken place.  You can say you "know someone" who is in a difficult situation and scared of retaliation (you don't have to tell them that you are the person).
You do not have to initiate legal proceedings or lodge a formal complaint or anything--I just think you need to, as soon as possible, start collecting the kind of documentation that a lawyer has told you will carry weight in court, just in case it ever comes to that.
I am guessing from this discussion that you are an attractive, intelligent woman in a technical field.  That is going to generate (sometimes intense) interest in you from many men in your field.  I'm not saying this as anything other than an observed fact--a reality that you need to be aware of.  These men are going to be all over the spectrum--really a two dimensional "spectrum", where you have an axis of social awkwardness where people sincerely don't know that what they are doing constitutes an inappropriate advance (yes, some of us really are that clueless), and an axis of just plain evil where there are some people that deliberately use their positions of power to take advantage of people.
In addition to the fact that people will be attracted to you, some will be threatened by you because you're a woman with rival superpowers that they associate with their manhood (pathetically sad, I know, but true).  Some will be neither attracted nor threatened themselves, but jealous of the attention paid to you by those who are attracted.
Subject to consulting with a network of women (I'm referring again to espertus ' advice) to see if anything I suggest below makes sense or matches their experience, it seems to me that you need to make sure that you recognize a few facts:

Your working relationship has already been damaged.  It's not that you're worried you might damage the relationship.  Your advisor's actions have damaged it.  You are looking to mitigate that damage.  It is not possible to avoid it.  The reason I'm saying this is that you might be afraid to take any action lest you "break something".  I don't think you will make good decisions if you have "fear of messing up the relationship" topmost in your mind.  You have a messed up relationship now, you are trying to salvage what you can of it without making it worse.
You need to be your own best defender and advocate.  You are in school to learn.  It is unfortunate that you are also having to learn this.  But you are likely to need it in situations after school (again, check with knowledgeable tech women before believing me, but I believe women in tech widely experience this).  Right now, start learning how you intelligently defend yourself in apparently impossible situations where someone else has all the power.  Note how espertus balances the fact that you have an absolute right not to be victimized with the fact that anything you do that looks like an attack to your advisor could be dangerous to you.  That does highlight how difficult your situation is, but if this were an easy situation, you'd already have figured it out.
Because of point 1 and some of point 2, you need to manage your own expectations.  You are probably not going to find a magical solution that simply lets you get everything you should be able to (professionally given academic guidance) from your advisor and nothing you shouldn't (unwanted advances).  Quit even thinking about there being a perfect way out and figure out what makes the most sense for you in your situation.
Even though it is not your fault, and you should not be the one that has to change your behavior to accommodate his bad behavior, I think you have to look at ways to manipulate space and time in such a way that your advisor simply has fewer opportunities to do the bad things he is doing.  Change either the hours that you are there or the place where you work.  This is not optimal, but the combination of his position of power and bad actions have created a sub optimal situation that you need some kind of practical response to.  Consider whether there might be a way to arrange your schedule or workspace to make it really hard for him to "casually drop by".
Lastly, I'm really, really hesitant to suggest this, but it seems possible to me that your co-advisees, if you know they can be trusted, could be natural allies.

A while ago I heard that his PhD student suggested to him that he
  spends too much time with me. He laughed and said it's not his
  business, and that we are working hard on some novel research method.

Do you know this student?  Were they possibly trying to helpfully intervene on your behalf or were they jealous of the time?
Although you are natural competitors for your advisor's time, you are also natural allies in that it's best for all of you if the advisor is as professional as possible.
Are you working on similar enough things that it would make sense for you to have a study group of some sort with the other advisees?  I'm guessing that it's an every-man-for-himself-trying-to-outshine-the-others kind of environment, but if it's not, developing a closer working relationship with them might give you allies in this other battle.  And, unlike the "get a fake boyfriend" suggestion, having a good relationship with these people actually makes real sense since they are in your field and people you could gain advantage from being able to network with later.

I wish I had better suggestions.  Possibly if you look for solutions that emphasize only the things you both agree on.  You both want your academic work to be successful.  So, if you need to make excuses not to spend time in pointless (to you) chit-chat, make every excuse be about your work.  "I don't want to be rude [note: this is true!  It would be so much easier if he wasn't making you do this], but I need to get back to working on the miniaturized earthworm defibrillator test results [also true!  You do need to get to work on those!  And, theoretically, something he agrees you should be doing.]."
Another strategy in the same vein--if he is forcing you to have conversations, you work to force the conversation back to work.  He has decided he is going to be in your space.  You decide that you are going to use that to your advantage by picking his brains about your project.  Have a list of questions ready at all times, on your phone or in your desk or on a whiteboard.  "That reminds me, I wanted to ask you about X."
Maybe time tracking software could be of use.  There is stuff out there that lets you click something saying you're working on task 1, then if you switch to task 2, you select that task and it starts tracking your time as applying to that (people like lawyers or freelancers will use these to know who to bill for what amount of time when they have multiple projects going).  Have actual tasks that apply to your project, and an array of non-project stuff: "at gym", "eating", "water cooler talk".  Don't even mention it, just start tracking all your time like that and looking at the results.  Once you have a good body of data from a couple of weeks, you can set goals of reducing your "water cooler talk" time--strictly because you want to increase your productivity--and then use that as a way to say you need to get back to work or you will miss your target [again--a real target, that is really about your project.  No pretense to maintain, simply an effort to get more work done].
Let me re-emphasize the fact that you should not have to do this.  I am not suggesting that bad things are happening because you aren't being assertive enough.  It is not your fault that he is making you come up with these strategies.  But I think it will be best for you, in both the short term as as a precedent that you set for yourself for the future, that you always assert whatever control you can, even when the power structure in a relationship is highly asymmetrical.

My condolences for a very unpleasant and difficult situation. A few extra hints that may add to what has been already said and they are comparatively low risk.

body language, attitude and physical interactions matter. Their effect may even be more powerful than any words that would be exchanged. So, for instance, if someone gets too friendly, position chairs and tables in a way that makes it difficult for him to come too close. Sometimes, if people are (perhaps culturally, but also for other reasons) coming too close for comfort, there is a way of jutting out the leg in an oblique fashion to generate some distance (you have to practice that so it doesn't look like an invitation). There are implied rules of entering someone else's space, and if we create an additional cost (in terms of cognitive steps) to invade this space, it creates a subliminal discouragement to do so.
Interact blandly and boringly. Some women may have an extraordinarily radiating aura that many men cannot withstand - I have known women like that, and they kept complaining about inappropriate advances by men which I am fully convinced were not invited by them (i.e. were not frivolously provoked); in one of the cases, I also happened to know one of the guys who complained about her and how she would toy with men (which was patently untrue - it was a fundamental misunderstanding on the side of the guy). If you would work in show business, you would, of course, capitalise on such a charisma. But, alas, you are a scientist, so it doesn't do you any good. But since that means that it is not your capital, either, you can play yourself down, be boring, wear boring clothes, forgo any adornment. Keep these for your free time. Note that I am not implying at all that you are inappropriately dressed or behave inappropriately, but by being deliberately uninteresting and bland you may counteract your over-effective charisma (if that is behind it).
In company with your supervisor, discuss and talk without enthusiasm, just blandly and neutrally, but competently (after all, you want to keep your scientific reputation).
When you are asked to be photographed, you can request that you do not wish your photo to be taken, because in today's time there is no way to control where the photo circulates. You may make the point that you do not furthermore wish to add another datapoint to existing face recognition algorithms (assuming you do not have a spate of photos on Facebook or elsewhere already). Or else, you say that you do not like yourself on photographs and do not like photos to be taken from you except for special family functions (or whatever plausible exception holds for you).
Note that in the supervisor, there are many aspects that may play a role in parallel - the feeling of superiority, but also the belief that he may ultimately win you over against your resistance; unfortunately, it is not infrequent that man-women interactions operate exactly like that and for many men genuine disinterest/reluctance is not easily discernible from a purely tactical hold-off. Since any open declaration of disinterest from your side in the present case will force his hand and may put him into the corner (which is the reason that you should also follow the earlier advice on building alliances), turning yourself from a desirable to a bland  personality with an unattractive appearance (only outwardly and temporarily, until you are through) may make him lose interest which is more effective and less damaging than trying to actively hold him off. I know cases where this has worked. If he should remark why you do not wear nice clothes anymore etc. you just say that in your current phase you have far too much to do to care about them.
Will adapting your personality ruin your quality of life? Yes, it will, but only temporarily and, given the constraints you have, it might give you a reasonable chance of getting through it with limited damage without compromising too much on the other constraints of yours. You need, for this, to be prepared for a long-haul, as this routine will take time to establish.

It is a terrible situation.
My first suggestion is change your supervisor. You don't need to explain why. Find someone in the department whose research is interesting to you (yes, it might not be as interesting as what you work in right now but I am sure there is something that is interesting). Start attending their group meetings. I don't think it worths the mental energy to sustain a long term professional relationship with your current advisor.
My second suggestion would be to find a senior female faculty member in your department that you can trust and discuss the problem with her.

All the answers are fine. However all of them are related to the answerer’s personality and I assume the questioner can't replicate that exact personalities or some answers suggest to do something that the questioner doesn't want to perform like, skipping, changing field or research.
From my point of view, this question is a common among most employed women. However as per my experience, if you take any step to get confront the advisor by discussing about this problem directory would make him mad. Also even if you follow the professional protocol to follow this issue, the situation would cost even your career as you said. However the end result is based on person to person.
There could be lot of ways to solve this.
However in here I'm suggesting an one method to neutrally stabilize the situation. however this method is framed with some criteria.
Tips to neutrally stabilize the situation:

What if an annoying car seller tries to sell a car and calls you all the day? Without complain to any law authorities or whatever, the easiest thing that you could do is to show him what you currently own and you don't prefer a new one.
If you got a partner or just a boy friend, this can be solved very easily. Or if you are currently not up to any relationship just ask some help from a close male friend. (For now lets call this guy as your partner)
Safest play would be to show up some basic personal stuff over your social media, FB, instagram in very neutral manner. Like the dinner's you both gone out, etc.
Or ask your partner to take a visit at university, or you could introduce him to the advisor.
When the advisor is around, Ask your partner to pick-up you after work.
Also if you could show up a photo of your partner's or of your both on your working desk, noticeable wallet or on pendant would be another good idea.
When the advisor is talking about non-work related personal stuff, you could respond to those topics like , "as my boy friend says like this, like that"
He will indirectly know that you value your personal stuff.
Let him know that you are not your own and there are people around you to support, protect.

My suggestion is to continue work with him as usual and eventually you could indirectly let him know that if he's up to a such a relationship, that you are not available and you are occupied.
Also he will eventually know that he doesn't have any chance and retreat without any hate. However this depends on the person's personality.
Expect the good side.
Good Luck!

In my experience, the most common outcome of the technique you propose, when applied to someone like this advisor who does not respect boundaries, is that then he starts asking you a whole lot of very uncomfortable questions about your boyfriend and the relationship.

@ff524 I tend to agree that this is not the most desirable technique, the involved individual might probably in the "best case" just leave it at asking uncomfortable questions, I find it likely that he'll assume a more stalkative attitude and in the worst case become even vindictive

@ff524 When I was composing i detailed, method is up to meet with a certain criteria. If the questioner up to this method. She doesn't want to lie. Just explain certain things to get rid of the main problem. Your down vote doesn't make any sense.

@ff524 : If someone asks you uncomfortable questions, you don't have to answer them.

@Christian the point isn't that one would have to answer inappropriate questions; it's that one feels uncomfortable at being asked them.

Terrible advice.  Using 'I already have a boyfriend' as if it's the reason one is not interested in a romantic relationship with someone can make it sound as if one might potentially be interested if the current relationship were to cease to exist.

The logic is. "I'm not available to any. So would you mind stopping the harassment?" This is for getting rid of the problem without making any one put in angry with the questioner. @TaraB your answer above is useless. Because questioner already says that "saying No to the advisor" is the problem she is having. So its ridiculous to answer her question to "Say NO". Also we are not here to fulfil any religious philosophy to tell the questioner that you need follow a 100% truthful way to get rid of the problem. She needs to keep the officer as normal, not enemy.

@inckka:  I don't think you can tell whether or not my answer is useless to the OP.  Sometimes people have difficulty saying no because they think they need to justify their refusal.  So if that happens to be the OP's case, then maybe realising that a simple 'No' is perfectly acceptable might help.
My recommendation not to follow the 'I have a boyfriend' advice given by you and others is not grounded in any religious philosophy, I simply believe that it is an unhelpful way of dealing with the situation and perpetuates the idea that women are 'available' unless already 'taken' by a man.

@Tara B Its kind of making sense like your answer and the comments for others and the votes are based for invalidate the argument of 'women are available unless already taken' . however I didnt answer for fulfill any argument. have posted a possible solution to solve the issue in peace. In societies, people are doing such kind of white lies to solve there problems in good manner. Whether the answer's path is black or white, if the questioner get the what she 'asked' and also she doesn't want to do what she clearly mentioned what she dislikes(say no), then that would be a helpful answer.

I  think your phrasing "you are not your own" is very telling. I am my own and will always be, though I've been married over 30 years. I can say no to any invitation on my own strength, and not because I am someone else's property who's not authorized to accept that invitation.

Worst advice ever. I think your points are pretty vague and can easily be misinterpreted.

authors: Θοδωρής Φλώκος


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Should I apologize/provide reasons when I resubmit after sitting on a referee report for 14 months?
I submitted an article for peer review early last year and received a referee report (major revisions) a few weeks after that. I've finally prepared a rebuttal and revisions to the article, after about 14 months have passed.
I plan to resubmit the article nonetheless, partly because the editor reached out (a year ago) encouraging resubmission.
When I submit the rebuttal and revisions, should I apologize and/or provide reasons for the delay to the referee and editors? Or should I just ignore the delay and resubmit like nothing happened?

Additional context:

The field is physics, the journal is Physical Review A.
The delay in my response is not because the response/changes took a lot of effort. The changes took about week of work cumulatively and this will be evident to reviewers/editor.
The main reasons for the long delay are, in order:

Some combination of procrastination issues and academic burnout.
My contract ended with the institution where I did this work and the work at my new employer was pretty intense.
I switched subfields and completely lost interest/momentum in the project.

I submitted my first solo paper in August. Got my first round of review in November. Haven't submitted back since (just an RR). Why? Busy! I'm still in school. And the editor told me "Better wait and submit it right, than to submit it too soon with too little progress". So, no need to apologize. Life is busy, and academia generally gets that. I would apologize, IF you said you'd get it in by a given deadline, and didn't. But, if there's no deadline..... then it isn't a very big deal, unless the editors say so.

The first two things that would cross my mind on receiving your revision would be:

I wonder if there are more recent developments in the past year, and if the authors have included these in the article.
This article is not likely to be groundbreaking, or the author would not take this long to revise.

Neither of these things would be affected by whether you apologized, so don't agonize over this. You could apologize (and there can be no drawback for apologizing), but nobody will get angry if you don't.

Thanks. I'll definitely address (1) by updating references in the resubmission. I think (2) probably(?) doesn't apply since our article (and most others in our subfield) was posted as a preprint before initial journal submission.

@forky40 for (2) I mean it's not likely to be a high impact paper - the kind that revolutionalizes the field, for example. Whether a preprint exists seems at most tangentially related.

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Non academic career for PhD in Biology
This question has asked previously for PhD in mathematics and computer science in this StackExchange forum. However, the situation will be completely different for Biology graduate because of the skills we learn during our PhD. Math and CS graduates have lot of open options (?) looking at their quantitative reasoning skills, which are not enough for biology. We learn lot of logic, reasoning and statistics, but is that enough to survive in a highly competitive world?. So I was wondering: is there any alternative career option for PhDs in biology?
P.S: There are few options I am already aware of, like teaching in school/university, quality control posts at various firms, R&D in pharmaceutical companies. I was wondering if there are any other options which are not very obvious from our skills.
Update (18 Sep 2015)
After reading comments and answers, Following more options have raised

Science communication
Librarian
NGO and firms for data analysis

This belongs on Workplace@SE, since it's about finding non-academic jobs.

I think this forum is more appropriate audience to answer this question.

There have actually been some studies (if I recall Mike The Mad Biologist's blog covered them awhile back) suggesting that biology graduate students are somewhat less happy than their peers because many of the specialized skills they pick up aren't immediately transferrable. For some aspects of "biology" this isn't true - for example, a mathematical biologist is likely just as qualified to exit into a quantitative field as an applied mathematics student, some fields of biology involve code, etc.
Failing that, some other options colleagues who are biologists have pursued:

Government positions. Some of these are "academia-lite", some of them are markedly different, but there are several branches of government that hire biologists in some form.
Teaching at the high school level. You're likely overqualified, but that's not a bad thing, and there are private high schools that very much value "X% of our faculty have PhDs..." as something to tell parents.
As you mention knowing exist already, there are biotech companies that exist, and employ biologists in many capacities.
Conservation organizations, private foundations, etc. may be of interest, especially if you're more ecology oriented.
Depending on your research area, what you did, etc. you may be able to brand yourself as a "data scientist" - at the moment it's pretty vague as to what exactly that means.
Science communication - university offices that do outreach, news organizations, etc.
With the addition of an MLS, a career as a research librarian is also potentially an option.

Ah, Science communication. I have totally forgotten about that :)

In general, the options for biology are very similar to those of other fields---the answers on the computer science question you linked mostly apply quite well to any STEM discipline (with the possible exception of finance companies).
The one important caveat that I would add for Ph.D. students in the biomedical field, however, is to make sure you self-advocate and ensure that you are really getting educated as a scientist, not exploited as a lab technician.  This can happen in any field, but anecdotally seems to be much more common in biomedical fields, and is extremely variable from lab to lab.  Some labs are very good at giving their students a complete scientific educations, others (and it seems most likely to happen in big labs) mostly want somebody to run assays at the bench, and one can finish a Ph.D. with very little of the knowledge that non-academic employers may expect you to have.

The options which CS link is refereeing generally involves skills which computational biology or theoretical biology graduate can easily tackle. I don't know how molecular biologist can fit into those profile.

@Dexter I'm not sure why you think a molecular biologist can't work for places like a government lab, a contract R&D organization, a consultancy, or a startup company.  Places like that do molecular biology work too.

That's true. I was just expecting some more options.

@Dexter There's actually a lot of options there---there's a bazillion interesting and unusual niches.  It just takes some work to find them and figure out which ones make sense for you, as well as general skills in problem solving, critical thinking, and communication that should be learned in any Ph.D. program.

@jakebeal by communication, what skills you include? in general what that mean? "having skill in communication.

@SSimon Being able to make one's ideas, proposals, and contributions understandable both to key individuals and to broad audiences and in both written, image, and verbal forms.

Oh, I see, @jakebeal yes I agree, but isnt it expected that from everyone who have university degree?

@SSimon While I believe that it should be a strong part of every education, many universities do not have effective programs ensuring that it is so.

that is sad, usually if you dont develop these skills most of jobs opportunities will be close for you, maybe these univesrities thinks students dont need these?

@SSimon Intending students to learn a skill is very different from preventing those who think it unimportant or daunting from skiving out on learning it.  For example, my undergraduate institution attempted to give students breadth through humanities requirements, but students who didn't want that found ways to take the most "math humanities" they could, such as management, economics, and philosophical logic.

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Letter of recommendation for grad. school application source
I am applying for admission to the Master's program next fall. However I am in doubt about the source of reference. I have two options:

My mentor at a research institute who was pursuing his PhD. when I was a research intern. However, he did not complete his PhD.
Research Scientist(PhD) at my current organization where my role is that of a software developer. Therefore the recommendation is based on my work as a developer rather than on my research contributions.

Both are willing to write strong recommendations for me.
Who would be a better source of recommendation?

Many applications require (or allow) more than one reference.  Is that not your case?

I need 3 recommendations.  2 professors from my undergraduate institute are recommending me.

Are you sure you can't include four recommendations? Many application management systems will allow for additional materials. You can ask the graduate school whether they will allow this.

I would ask mentor #1 (with a master's degree) to write a letter to the PhD research scientist #2, and have the latter (#2) submit a letter for your application. Thus, the recommendation letter is received from a prestigious source, is based on current experience of your work habits and character, but can also incorporate quotes/details from the more junior person. This is not an unusual pattern in my experience.

I would use the first person because it is about your work in research. I think that their qualifications matter very little: What really matters is the nature of your work when you were under their supervision.

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How are scientific papers uniquely identified?
Some papers have the Digital Object Identifier (DOI) which uniquely identify them, some other have an oai identifier (e.g. oai:arXiv.org:1402.3722). Even though I inspected the metadata of different sources like core, microsoft academic, and semantic scholar I couldn't find a unique identifier which is used among all sources of research papers.
How are all scientific publications uniquely identified?

Are you looking for unique identification by authors, publishing houses, librarians or the world?

What makes you think such unique identifiers exist?

I suggest revising (in the title and body) "How are all scientific publications uniquely identified ?" to "Are all scientific publications uniquely identifiable?" or "Is there a system to uniquely identify all scientific publications?"

"How are all scientific publications uniquely identified?" For citation usually by a combination of (title, journal, issue, pages, year, authors, doi, ...).

CORE and SemanticScholar definitely use DOIs, what do you mean that they don't?

It'd actually be nice to have unique identifiers for research papers that are like QR codes or just a simple string hash of a limited length. Hopefully that'd make citations a lot easier. It's currently annoying to have to type out all author names, volume numbers, date of publication etc.

@Nav "Hopefully that'd make citations a lot easier." Not if it would be another DOI system that is adopted by only a fraction of the total market. Also, at least for me, author+journal+year is sufficiently unique and easier to remember than any qr code or string hash. Just imagine you would see string hashes printed on slides during a talk. The DOI is already quite good and maybe there is or one can do a QR code version of it.

@Nemo This paper, for example, from CORE does not has a DOI. (https://core.ac.uk/display/25003332?recSetID=d9c639afdcbaf0492e75f0b426b67c6a::5bd343dca27930.34862522)

@Agelos the link doesn't work, but yes, CORE does not create DOIs for items, it uses the DOIs assigned by publishers.

Research publications predate the digital age, so only a fraction has a digital identifier. The unique identifier traditionally used is the full citation, of which various formats exist to suit discipline-specific needs. It is very likely for a full citation to be unique.
(However, automatic data analysis may not be able to recognize the identity of diffently formated citations of the same publication. That's DOI's strong suit.)

I’m not sure I agree with the reasoning: books predate the digital age, yet even those books (up to a point) all have digital identifiers (ISBN for most of them, and other — albeit not uniform — identifiers for older works). Likewise, older publications can be (and are) digitally archived and identified in retrospect.

@KonradRudolph First, I think there's an overloading of the word "digital" here. ISBNs were introduced as an ISO standard in 1970, and while they (and other serial numbers) consist of a series of digits (one meaning of 'digital'), this was certainly before the "digital age". Second, I agree with you. I also don't see any particular reason why a DOI-like number for research papers couldn't have been introduced way before 2000, say in the early 1900s. There probably wasn't much need for it, but it could, in principle, have been done.

@Anyon This overloading was inadvertent: You’re right that analog ISBNs were already sequence of digits (i.e. “digital”) but I was actually referring to the fact that they are nowadays digitised.

@Anyon, Konrad Rudolph, you're both correct, but the need for unique IDs presumably is a result of digitization in the sense of computerization, since computers don't deal well with the ambiguity of traditional citations.

I think the key piece of this answer is the parenthetical at the end: the unique IDs aren't for "us", they are for our digital underlings and future overlords to prevent them from making mistakes. All of the other citation stuff is for "us" and is sufficiently unique going back a long time.

@BryanKrause "...the unique IDs aren't for "us".." If they aren't for us then the obvious solution are just hashes of the electronic files. Makes everything universally (almost always) uniquely identifiable. It probably depends on what the current digital underlings and future overlords intent to do with these scientific publications.

@Trilarion The problem is, by definition, hashes completely change in cases where the actual content has not. When PDF becomes obsolete and papers get converted into whatever new format, you'll get a change... Some publishers put a cover page on papers with an ad, or they watermark the paper with the downloading IP, also causing changes. DOIs don't have this issue by not assuming binary representations = content.

I work at Crossref and we run a registry of DOIs with attached metadata beyond such as funder acknowledgements, whether it's been retracted, etc. Our DOIs (about 100 million) are specifically citation identifiers and also persistent links. DOI is also the ISO standard for identifying research publications. 11,000 publishers use Crossref but yes they have not all gone back to their print archives to digitise them and assign DOIs yet, books especially are lagging behind. It integrates with DataCite DOIs for data and software citations (about 10 million of them), and with ORCID iDs which identify authors & contributors (about 5 million so far). There is also ROR.community starting up to uniquely identify research institutions. All these are open community-governed nonprofit organizations. ArXiv is pretty much the only publisher that doesn't (yet) use DOIs. Centre for Open Science does for all the other 'Xivs', as does BioRxiV etc.

Of course papers on the arXiv are "published" in a loose sense of the word ("made public"), but at the moment a DOI usually seems to indicate that a paper is published in a stricter sense (e.g. published in a peer-reviewed journal)...?

@Earthliŋ It's worth noting your example is neither necessary, nor sufficient, since multiple organisations will issue a DOI for non-peer reviewed papers (or non-papers) and there are journals offering 'peer-review' (in small fields, sometimes legitimately) which aren't authorised issuers of DOIs.

Hi @Earthliŋ, there are millions of DOIs for lots of non-peer-reviewed and less 'strict' stuff, e.g. preprints, theses, reports, working papers, diagrams, component figures and charts, software, blog posts, peer review reports, even annotations/comments. Basically anything citeable.

How are all scientific publications uniquely identified ?

Formally, they aren't: There is no system to uniquely identify publications. But, author(s), year of publication, and title are typically sufficient to uniquely identify publications, because authors typically publish different works with different titles and it is unlikely that distinct author(s) with the same name(s) will publish in the same year with the same title. Moreover, it is even more unlikely once publication venue is added and distinct once page numbers are added (assuming no two publication venues share the same name in the same year). So, a full citation should suffice to uniquely identify publications, but there may exist (with low probability) publications that cannot be uniquely identified.
(Uniquely identifying authors of a publication is more problematic.)

"Moreover, it is even more unlikely once publication venue is added and distinct once page numbers are added." Including the page numbers should make it impossible to not uniquely identify the publication for all practical purposes.

@Trilarion That's why I wrote "and distinct once page numbers are added". Actually, thinking about it, that's not strictly true. Two publication venues might share the same name.

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U.S. universities on-campus residence for International PhD students?
I want to ask generally, do most U.S. universities offer on-campus accommodation for International Ph.D. students Who are married?
If the student is benefitted from scholarships {Free tuition and fees + 2k monthly stipend} will he/she need to pay an extra to use not-shared on-campus settlements?
Without any self-funding and other support, is the stipend enough to pay for it while taking care of food, health care, etc. at the same time?

I want to ask generally, do most U.S. universities offer on-campus accommodation for International Ph.D. students Who are married?

Probably not. Even when available, it might not be your best option. In some places on-campus housing can be a fair bit more expensive than renting from a private landlord. And if the university offers subsidized housing (whether on or away from the main campus) the waiting period can be quite long. Basically, you'd want to research your alternatives once you know where you might be going.

If the student is benefitted from scholarships {Free tuition and fees + 2k monthly stipend} will he/she need to pay an extra to use not-shared on-campus settlements?

Generally, housing wouldn't be free, but possibly subsidized.

Without any self-funding and other support, is the stipend enough to pay for it while taking care of food, health care, etc. at the same time?

It varies, so it's hard to say anything concretely. If the university pays for health insurance, that can be worth a lot actually. Also, living expenses vary considerably from place to place. I will say that if you have to pay for insurance yourself, and pay rent in a large popular city, well, money could be very tight.
Again, this is something you'll have to research when considering your offers. There are websites that help you compare these expenses between cities, to see if e.g. rent is particularly expensive somewhere.

If you do the following search on Google, you will find some universities that do: "married student housing for graduate students". But I doubt that most do and the ones that provide this service would be large universities. Housing isn't free, of course, but it can be priced fairly low. It is possible that it is market priced in some places and provided only for convenience, but I think that it is most likely subsidized by the university nearly everywhere it is offered.
I took advantage of this long ago so my experience is likely no longer valid, but the search will get you started. In my case it was very very low and included all utilities.

Without any financial support, is the stipend enough to pay for it while taking care of food, health care, etc.?

It is impossible to say. Note that a university big enough to provide a housing option will probably also have a fairly low cost medical insurance program. The US is a very expensive country generally, of course. You will have to do your own math.

In my limited experience, it has actually been the smaller schools that have provided more generous housing, often if they are in smaller towns and there's nowhere to live, versus universities in large cities where there are many options.